title: CGH-SANGER 3K 3

status: Public on Jul 31 2006

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

organism: Homo sapiens

technology: spotted DNA/cDNA

description:
The array contains 3588 distinct BAC and PAC sequences at an average resolution of 1Mb. The bacs were printed in 2 replicates.
3530 BACS are from the Sanger institute. 58 BACS were provided by K.U.Leuven Department CME (Belgium).
The bacs were amplified by DOP - PCR.
In total the array design contains 8112 features printed in a layout of
12 meta rows, 4 meta columns, 13 rows per block and 13 columns per block.

distribution: non-commercial

manufacturer: VIB MicroArray Facility Leuven (Belgium)

first: Paul

last: Van Hummelen

first: Joris

last: Vermeesch

manufacture_protocol:
Equipment:
1. Lucidea microarray spotter (Amersham Biosciences, Buckinghamshire, UK).
2. 384 microtiter plates (Amersham Biosciences, Buckinghamshire, UK).
3.  Motorola slides
Printing protocol
1. Set spotter settings : 55% humidity, column pitch = 317 um, row pitch = 317 um.
2. Make sure room temperature is between 20-24 degrees Celsius.
3. Place microtiter plates in the plate hotel with A1 in upper right corner.
4. Place 75 slides on the slide-deck and perform 2 manual pin-washes.
5. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vaccuum and humidity settings on. Continue spotting the next morning until all plates are printed.
6. Slides can be stored for at least 6 months in a dry-cabinet.


title: CGH-SANGER 5K 2

description:
The array contains 5088 distinct BAC and PAC sequences at an average resolution of 1Mb. The bacs were printed in 2 replicates.
3490 BACS are from the Sanger institute. 1152  BACS were provided by K.U.Leuven Department CME (Belgium).
and 96 BACS are from the Human 32K BAC rearray of CHORI BACPAC resources.
The bacs were amplified by DOP - PCR.
In total the array design contains 10080 features printed in a layout of
12 meta rows, 4 meta columns, 14 rows per block and 15 columns per block.

manufacturer: VIB MicroArray Facility, Leuven (Belgium)

first: Guy

last: Froyen

manufacture_protocol:
Equipment:
1. Lucidea microarray spotter (Amersham Biosciences, Buckinghamshire, UK).
2. 384 microtiter plates (Amersham Biosciences, Buckinghamshire, UK).
3.  Motorola slides
Printing protocol:
1. Set spotter settings : 55% humidity, column pitch = 272 um, row pitch = 272 um.
2. Make sure room temperature is between 20-24 degrees Celsius.
3. Place microtiter plates in the plate hotel with A1 in upper right corner.
4. Place 75 slides on the slide-deck and perform 2 manual pin-washes.
5. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vaccuum and humidity settings on. Continue spotting the next morning until all plates are printed.
6. Slides can be stored for at least 6 months in a dry-cabinet.


title: PIQOR 6k rat set1

status: Public on Jul 28 2006

city: Cologne

first: Bernhard

last: Gerstmayer

address: Stockheimer Weg 1

country: Germany

institute: Miltenyi Biotec GmbH

organism: Rattus norvegicus

description: The PIQOR 6k rat set 1 includes the two arrays PIQOR 348 and PIQOR 350 with a total number of 5957 rat specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer. The PIQOR array 348 contains 3000 cDNAs and controls spotted in duplicate. The PIQOR array 350 contains 2937 cDNAs and controls spotted in duplicate and 20 cDNAs  as sixfold replicates.

distribution: custom-commercial

first: B.

first: A.

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: Operon Rat Oligonucleotide Array

status: Public on Jul 21 2006

city: Tucson

first: Niranjan

last: Maitra

state: AZ

address: 1501 North Campbell Avenue

department: Sarver Heart Center

country: USA

institute: University of Arizona

technology: spotted oligonucleotide

manufacture_protocol: Unigene 70 mer Oligo Nucleotide Array


title: rzpd rat

status: Public on Jul 05 2006

city: Toulouse

first: Philippe

middle: V

last: Rouet

address: 1 Ave Jean Poulhes

department: Cardiology

country: France

institute: INSERM U1048

description: Rat Unigene 1 lib 953

manufacture_protocol:
Instructions for scoring high-density colony macroarrays 5x5 duplicate

Your macroarray consists of an array of duplicate clones arranged in blocks 5x5. After successful hybridization, on your autoradiograph duplicate spots should be visible, each representing one of the 12 duplicate spotting types within a block (please refer to RZPD document "Scoring template for colony macroarray 5x5 duplicate").

1) Preposition RZPD document "Scoring template for colony macroarrays" on a flat surface in front of you.

2) On this document, orientate your autoradiograph such that the lettering is at its top margin (please refer to RZPD document "Orientation of macroarrays") and match autoradiograph and template.

3) Note that the block at position 1;1 is located at the top left corner of the autoradiograph.

4) Starting from one pair of positive signals, determine the X;Y coordinates of the corresponding block (see also Diagram for Example).

5) Within the block, identify the coordinates of both signals (x';y' for spot and x'';y'' for spot duplicate) by comparing their positions with the 12 duplicate spotting types listed to the left of your autoradiograph (see also Diagram for Example).

6) Calculate the final x;y coordinates of both positive signals using the general sets of equations:

Spot: 	x1 = 5 (X - 1) + x' 	     	Spot duplicate: 	x2 = 5 (X - 1) + x''
	y1 = 5 (Y - 1) + y' 			y2 = 5 (Y - 1) + y''

	Legend 	Example
5 	5x5 spotting pattern 	5
X;Y 	X coordinate
Y coordinate
of the block
	X = 3
Y = 2
x';y'

x'';y''
	x' coordinate spot
y' coordinate spot
x'' coordinate spot duplicate
y'' coordinate spot duplicate
within a block
	x' = 5
y' = 1
x'' = 4
y'' = 4
x1;y1

x2;y2
	x coordinate spot
y coordinate spot
x coordinate spot duplicate
y coordinate spot duplicate
on the macroarray
	x1 = 5(3-1)+5 = 15
y1 = 5(2-1)+1 = 6
x2 = 5(3-1)+4 = 14
y2 = 5(2-1)+4 = 9

The coordinates of the clones of the example are x1 = 15; y1 = 6 (spot) and x2 = 14; y2 = 9 (spot duplicate).


title: Nicotiana benthamiana SuperSAGE Array des

city: Ueda

first: Hideo

last: Matsumura

state: Nagano

address: Tokita 3-15-1

department: Gene Research Center

country: Japan

institute: Shinshu University

organism: Nicotiana benthamiana

technology: in situ oligonucleotide

manufacture_protocol: SuperSAGE Array was produced by on-chip synthesis of 26-base long oligonucleotides exactly corresponding to the tag sequences (tag probe) by NimbleGen's photolithography technology6.  Oligonucleotides carrying two-base mismatches in positions no. 7 and 13 of 26-base SuperSAGE tag sequences were also synthesized on the array.


title: CGH-SANGER 3K 5

description:
The array contains 3696 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 3638 BACS are from the Sanger institute. 58 BACS were provided by K.U.Leuven Department CME (Belgium).
The bacs were amplified by DOP - PCR. In total the array design contains 7744 features printed in a layout of
4 meta rows, 4 meta columns, 22 rows per block and 22 columns per block.
This grid is printed twice on the glass slides allowing for two microarray assays per slide.

manufacture_protocol:
MicroGrid Printing Protocol
Equipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 16 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4. Codelink slides (cat#: 30001100, GE Healthcare).

Printing 2 arrays of 4x4 blocks on 1 microscope slide:
1. Dissolve PCR products in 125mM Phosphate buffer, 0.000125% sarcosyl at concentrations ranging between 300 ng/ul and array in 384 microtiter plates.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 60%; 120 spots per source visit.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 60 to 120 slides on the slide-deck.
6. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vaccuum and humidity settings on. Continue spotting the next morning until all plates are printed.
7. After spotting, incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.
9. Slides can be stored for at least 6 months in a dry-cabinet.


title: CGH-SANGER 3K 2

description:
The array contains 3492 distinct BAC and PAC sequences at an average resolution of 1Mb. The bacs were printed in 2 replicates.
3434 BACS are from the Sanger institute. 58 BACS were provided by K.U.Leuven Department CME (Belgium).
The bacs were amplified by DOP - PCR.
In total the array design contains 7488 features printed in a layout of
12 meta rows, 4 meta columns, 12 rows per block and 13 columns per block.

manufacture_protocol:
Equipment:
1. Lucidea microarray spotter (Amersham Biosciences, Buckinghamshire, UK).
2. 384 microtiter plates (Amersham Biosciences, Buckinghamshire, UK).
3.  Motorola slides
Printing protocol:
1. Set spotter settings : 55% humidity, column pitch = 317 um, row pitch = 317 um.
2. Make sure room temperature is between 20-24 degrees Celsius.
3. Place microtiter plates in the plate hotel with A1 in upper right corner.
4. Place 75 slides on the slide-deck and perform 2 manual pin-washes.
5. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vaccuum and humidity settings on. Continue spotting the next morning until all plates are printed.
6. Slides can be stored for at least 6 months in a dry-cabinet.


title: Pinus taeda cDNA

city: Raleigh

first: Chris

last: Smith

state: NC

address: 840 Main Campus Dr

department: Bioinformatics Research Center

institute: NCSU

organism: Pinus taeda

description: The microarray contains ESTs selected from 6 Xylem libraries: 1. NXCI - ESTs from juvenile compression wood of Pinus taeda (loblolly pine) 2. NXLV - ESTs from transitional/mature late wood of Pinus taeda (loblolly pine) 3. NXNV - ESTs from mature normal wood of Pinus taeda (loblolly pine) 4. NXPV - ESTs from transitional planings wood of Pinus taeda (loblolly pine) 5. NXRV - ESTs from root wood of Pinus taeda (loblolly pine) 6. NXSI - ESTs from juvenile side wood of Pinus taeda (loblolly pine) , a Pollen Cone library, and a Shoot tip library.

first: Aleksandra

last: Adomas

first: Gregory

last: Heller

first: Guosheng

last: Li

first: Ake

last: Olson

first: Tzu-Ming

last: Chu

first: Jason

last: Osborne

first: Debbie

last: Craig

first: Len

last: van Zyl

first: Russ

last: Wolfinger

first: Ron

last: Sederoff

first: Ralph

middle: A

last: Dean

first: Jan

last: Stenlid

first: Roger

last: Finlay

first: Frederick

middle: O

last: Asiegbu

manufacture_protocol: DNA from 2109 ESTs was printed in two replications onto amino-silane coated CMT-GAPS slides (Corning Inc; Corning, NY, USA) using a Lucidea Array Spotter (Amersham Biosciences, USA). After printing, the DNA was cross linked using 250 mJ of UV-C radiation. The slides were subsequently baked at 75ºC for 2 hrs.


title: MH Hannover Pseudomonas putida 4.5K

status: Public on Jul 27 2006

city: Hannover

first: Burkhard

last: Tummler

address: Carl-Neuberg-Str. 1

institute: Medizinische Hochschule Hannover

organism: Pseudomonas putida

manufacturer: DKFZ, The Multi-Conditional Hybridization Intensity Processing System (M-CHiPS)

first: Diana

last: Stjepandic

first: Kerstin

last: Bohm

first: Christian

last: Weinel

first: Oleg

last: Reva

first: Jorg

last: Hoheisel

manufacture_protocol:
Purified DNA of some 4600 overlapping shotgun clones in vector pCR-BluntII-TOPO (Invitrogen, Groningen, The Netherlands) was used as template in standard PCR amplification with the vector-specific primer pair d(TCGGATC CACTAGTAACG) and d(GGCCGCCAGTGTGATG). Shotgun cloning had been performed according to the procedures described by the vector's manufacturer. Each PCR reaction was individually checked by agarose gel electrophoresis. Prior to spotting onto microarrays, the DNA concentration of the fragments was adjusted to about 300 ng μl1. Spotting was done using an SDDC-2 DNA Micro-Arrayer from Engineering Services Inc. (Toronto, Canada) and SMP3 pins (TeleChem International Inc., Sunnyvale, USA) onto glass slides coated with poly L-lysine as described in detail earlier (Diehl et al., 2001).
For labelling DNA-samples, random priming (Feinberg and Vogelstein, 1983) was performed on 500 ng genomic Pseudomonas DNA in the presence of 15 μM each of dATP, dGTP and dTTP, and 25 μM Cy3- or Cy5-labelled dCTP (Amersham-Pharmacia, Amersham, UK). Hybridization of such samples to the microarrays was done as described (Diehl et al., 2001). Fluorescence signals were detected on a ScanArray5000 unit (Packard, Billerica, USA) and analysed with the GenePix software package (Axon Instruments, Union City, USA).


title: CSIRO Wheat Barley 5K endosperm (WHEAT BARLEY ENDOSPERM)

status: Public on Jul 25 2006

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

organism:
Hordeum vulgare
Triticum aestivum

description: Non-Redundant Set of genes expressed in endosperm

first: Bryan

last: Clarke

first: Sadequr

last: Rahman

manufacture_protocol: Clones were selected from three cDNA libraries for the construction of the microarray. These libraries were a non-normalised endosperm library from T. aestivum cv Wyuna (Clarke et al. 2000) and two normalised endosperm libraries; one from T. aestivum cv Hartog and the other from Hordeum vulgare cv Himalaya. The non-redundant set of cDNA clones were grown over night in 250 ml TYPGN medium, (20 g tryptone, 19 g yeast extract, 10 ml 80% (v/v) glycerol, 5 g Na2HPO4, 10 g KNO3 per litre) supplemented with 100 ?g/ml Ampicillin, in 96-well microtiter plates. These plates were replicated in 150 ?l of fresh medium and grown over night. The replicate plate was stored at -80oC after the addition of 100 ?l of 80% (v/v) glycerol. Plasmid preparations were made of the primary plate, following standard alkaline lysis procedures, and the inserts were amplified by PCR using the M13/pUC forward and reverse sequencing primers (New England Biolabs, Inc.). For quantitative and qualitative evaluation of the amplification procedure, 1 ?l of the PCR reaction was run on a 2% (w/v) agarose gel in Tris-borate buffer pH 8 and the image recorded. The remainder of the PCR products were ethanol-precipitated, resuspended in 6 ?l of 50% (w/v) dimethyl sulfoxide and transferred from the 96-well plates to 384-well microtiter plates for printing. The PCR products were printed onto CMT-GAPSTM coated microscope slides (Corning USA) using an Omnigrid Microarrayer (Genemachines, San Carlos, CA) with ChipMaker2 quill pins (TeleChem International Inc., Sunnyvale, CA). Prior to hybridisation the slides were baked at 80 OC for 2 hours.


title: RIPCM Ureaplasma parvum 1.2K RIPCM_UParvum_582

city: Moscow

middle: Victorovich

last: Klubin

address: ul. Malaya Pirogovskaya 1a

department: Departament of molecular biology and genetics

country: Russia

institute: Research Institute of  Physico-Chemical Medicine

organism: Ureaplasma parvum

manufacturer: Laboratory of post-genome methods in biology, RIPCM

first: Kuvat

middle: T

last: Momynaliev

first: Vera

last: Chelysheva

first: Oksana

last: Selesneva

first: Tatyana

last: Akopian

first: Vadim

middle: M

last: Govorun

manufacture_protocol:
1) PCR primer pairs were designed to amplify 613 ORFs of Ureaplasma parvum.
2) Amplification ORF
3) All PCR products were analyzed by electrophoresis on 1.5 % agarose gels
4) The ORF-specific PCR products were printed robotically in 4×4 double offset configuration onto positively charged nylon membranes in duplicate


title: Anopheles gambiae high density oligonucleotide microarray

status: Public on Jul 15 2006

city: Chicago

first: Joelle

middle: R

last: Perusse

state: IL

address: 920 E. 58th Street

department: Department of Genetics

institute: Yale University

organism: Anopheles gambiae

manufacture_protocol:
Probe selection:
The NASA Oligonucleotide Probe Selection Algorithm (NOPSA) (Stolc et al., 2004) was applied to select the optimal probes (36-mers) by screening the Anopheles genome. 1000 negative control probes were also designed to estimate the array non-specific binding background. The negative control probes were generated by joining 3 random 12-mers which have no match in the Anopheles genome.
From Halasz et al. Manuscript to be published in Genome Biology.
Array synthesis as in:
V. Stolc, Z. Gauhar, C. Mason et al. A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster. Science, in Science, (2004) 306(5696):655-60.


title: Medicago truncatula Genome Oligo Set

status: Public on Jul 20 2005

city: Ardmore

first: Bettina

last: Deavours

state: OK

institute: Samuel Roberts Noble Foundation

organism: Medicago truncatula

description:
The Medicago Genome Oligo Set Version 1.0 (Qiagen Operon, Alameda, CA) includes 70-mer oligonucleotides representing 16,086 M. truncatula tentative consensus sequences (TCs) from The Institute of Genome Research (TIGR) Gene Index Database (www.tigr.org/tdb/tgi/mtgi/) MtGI Release 5.0 as well as both positive and negative controls.  Details of this oligo set are available at http://oligos.qiagen.com/arrays/omad.php.  The oligos were spotted in 3x SSC onto Superamine (Telechem) glass slides by the Galbraith lab at the University of Arizona (Tucson, AZ).  A single array element was printed per oligo.  After printing, slides were baked at 80°C for 1 hour and stored at RT.
Keywords = Medicago
Keywords = legume

first: David

middle: W

last: Galbraith


title: CGH-SANGER 3K 1

first: Rekin's

last: Janky

description: The array contains 3529 distinct BAC and PAC sequences from the Sanger institute at an average resolution of 1Mb. The bacs were amplified by DOP - PCR and printed in 2 replicates. In total the array design contains 7488 features printed in a layout of 12 meta rows, 4 meta columns, 12 rows per block and 13 columns per block.

first: Paul

last: Van Hummelen

first: Joris

last: Vermeesch

manufacture_protocol:
Equipment:
1. Lucidea microarray spotter (Amersham Biosciences, Buckinghamshire, UK).
2. 384 microtiter plates (Amersham Biosciences, Buckinghamshire, UK).
3. Motorola slides
Printing protocol:
1. Set spotter settings : 55% humidity, column pitch = 317 um, row pitch = 317 um.
2. Make sure room temperature is between 20-24 degrees Celsius.
3. Place microtiter plates in the plate hotel with A1 in upper right corner.
4. Place 75 slides on the slide-deck and perform 2 manual pin-washes.
5. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vaccuum and humidity settings on. Continue spotting the next morning until all plates are printed.
6. Slides can be stored for at least 6 months in a dry-cabinet.


title: CGH-CHROM14 2K 2

description:
The array contains 1560 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 722 BACS are from the Sanger institute. 838 BACS from chromosome 14 are from the Human 32K BAC rearray of CHORI BACPAC resources. The bacs were amplified by DOP - PCR. In total the array design contains 3328 features printed in a layout of 4 meta rows, 4 meta columns, 13 rows per block and 16 columns per block.
This grid is printed twice on the glass slides allowing for two microarray assays per slide.

manufacture_protocol:
MicroGrid Printing Protocol
Equipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 16 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4. Codelink slides (cat#: 30001100, GE Healthcare).

Printing 2 arrays of 4x4 blocks on 1 microscope slide:
1. Dissolve PCR products in 125mM Phosphate buffer, 0.000125% sarcosyl at concentrations ranging between 300 ng/ul and array in 384 microtiter plates.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 280 um, row pitch = 280 um; Humidity 60%; 120 spots per source visit.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 60 to 120 slides on the slide-deck.
6. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vaccuum and humidity settings on. Continue spotting the next morning until all plates are printed.
7. After spotting, incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.
9. Slides can be stored for at least 6 months in a dry-cabinet.


title: Swegene Human 27K RAP UniGene188 array

status: Public on Jul 12 2006

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

first: Ake

last: Borg

manufacture_protocol: Arrays were produced by the Swegene DNA micro array resource center at Lund University by using amplified cDNA targets from Research Genetics clones. Target amplification was performed using PCR and cDNA products were verified by agarose gel electrophoresis and purified by size-exclusion filtration. After purification, cDNA was recovered in water, adjusted to 50% DMSO and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics) equipped with MicroSpot2500 pins (BioRobotics).


title: Vysis GenoSensor CGH Array 300

city: Tel-Aviv

first: Anat

last: Bar-Shira

address: 6 Weizmann St.

department: Genetic Institute

country: Israel

institute: Tel-Aviv Sourasky Medical Center

description: The genomic array contains 287 targets, each spotted in triplicate.  Permits the screening of pronto-oncogenes, tumor suppressor genes, microdeletion syndrome gene regions and subtelomeric regions.  Clone verification has been accomplished by confirming each clone on the microarray with fluorescence in situ hybridization (FISH) mapping and PCR with gene specific primers.

manufacture_protocol: see manufacturer's website


title: University Health Network Yeast 6.4K Array (Y6.4K)

city: Mississauga

first: James

middle: B

last: Anderson

state: Ontario

address: 3359 Mississauga Road N.

department: Biology

country: Canada

institute: University of Toronto

organism: Saccharomyces cerevisiae

description: There are a total of 48 grids. There are 17 spot rows and 16 spot columns in each of the 48 grids. Centre to centre distance between spots is 200 micrometers and grid to grid distance is 4500 micrometers

manufacture_protocol: Microarrays are printed on GAPS II or UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use. Double-spotted array containing 6,240 yeast ORFs (plus control spots totalling 6.4K).


title: EJH FT LVS iron restriction

status: Public on Jul 26 2006

city: Dallas

first: Eric

middle: J.

last: Hansen

state: TX

address: 5323 Harry Hines Blvd.

department: Microbiology

institute: UT Southwestern Medical Center

organism: Francisella tularensis

first: Kaiping

last: Deng

first: Robert

middle: J

last: Blick

manufacture_protocol: The oligonucleotides were synthesized by Qiagen and spotted in triplicate on Corning UltraGapII slides.


title: Rice SuperSAGE Array1

first: Hideo

last: Matsumura

organism: Oryza sativa

manufacture_protocol: SuperSAGE Array was produced by on-chip synthesis of 26-base long oligonucleotides exactly corresponding to the tag sequences (tag probe) by NimbleGens photolithography technology6.  Oligonucleotides carrying two-base mismatches in positions no. 7 and 13 of 26-base SuperSAGE tag sequences were also synthesized on the array.


title: CSIRO NSW-AGC Wheat Barley 22K Array

first: Andrew

last: Spriggs

description: 22K Wheat cDNA Array

first: Bryan

last: Clarke

first: Damien

last: Platten

manufacture_protocol: Clones were selected from the following cDNA libraries for the construction of the microarray. These libraries were a non-normalised endosperm library from T. aestivum cv Wyuna (Clarke et al. 2000) and two normalised endosperm libraries; one from T. aestivum cv Hartog and the other from Hordeum vulgare cv Himalaya.  Approximately 6,000 EST clones, mapped to the wheat genome, kindly supplied by O. Anderson, Western Region Research Centre, USDA, 800 Buchanan St., Albany, CA 9471 USA. A unigene set of 9,000 EST clones from Bristol University (see cerealsdb.uk.net website for details of the libraries used). Kindly supplied by Keith J. Edwards, School of Biological Sciences, University of Bristol, Woodland Road, Bristol, BS8 1UG, UK. A collection of 400 ESTs from drought stressed wheat seedlings, kindly supplied by Heather Way and Xue Gang-Ping, CSIRO PI, St. Lucia, Brisbane, Australia. The non-redundant set of cDNA clones were grown over night in 250 ml TYPGN medium, (20 g tryptone, 19 g yeast extract, 10 ml 80% (v/v) glycerol, 5 g Na2HPO4, 10 g KNO3 per litre) supplemented with 100 ?g/ml Ampicillin, in 96-well microtiter plates. These plates were replicated in 150 ?l of fresh medium and grown over night. The replicate plate was stored at -80oC after the addition of 100 ?l of 80% (v/v) glycerol. Plasmid preparations were made of the primary plate, following standard alkaline lysis procedures, and the inserts were amplified by PCR using the M13/pUC forward and reverse sequencing primers (New England Biolabs, Inc.). For quantitative and qualitative evaluation of the amplification procedure, 1 ?l of the PCR reaction was run on a 2% (w/v) agarose gel in Tris-borate buffer pH 8 and the image recorded. The remainder of the PCR products were ethanol-precipitated, resuspended in 6 ?l of 50% (w/v) dimethyl sulfoxide and transferred from the 96-well plates to 384-well microtiter plates for printing. The PCR products were printed onto CMT-GAPSTM coated microscope slides (Corning USA) using an Omnigrid Microarrayer (Genemachines, San Carlos, CA) with ChipMaker2 quill pins (TeleChem International Inc., Sunnyvale, CA). Prior to hybridisation the slides were baked at 80 OC for 2 hours.


title: Thellungiella EST array

status: Public on Jul 22 2006

city: Waterloo

first: Barbara

last: Moffatt

address: 200 University Ave West

institute: University of Waterloo

organism: Eutrema

first: C

middle: E

last: Wong

first: Y

last: Li

first: A

last: Labbe

first: P

last: Nuin

last: Camino-Diaz

first: B

last: Whitty

first: D

last: Guevara

last: Golding

first: E

last: Weretinylk

first: M

last: Griffith

manufacture_protocol:
a)PCR Amplification from EST Clones
b)Purification of PCR products
c)Spotting the Arrays
d)Processing Spotted Arrays


title: Codelink Mouse Uniset I Bioarray

city: Atlanta

first: Michelle

last: Sykes

state: GA

address: 101 Woodruff Circle, Rm. 2001

department: Biomedical Engineering

institute: Georgia Institute of Technology and Emory University

organism: Mus musculus

middle: C


title: Malaria Oligo p19

status: Public on Jul 11 2006

city: San Francisco

first: Joseph

middle: L

last: DeRisi

state: CA

department: Biochemistry and Biophysics

institute: University of California San Francisco

organism:
Saccharomyces cerevisiae
Plasmodium falciparum

description: Plasmodium falciparum coding specific 70mer oligonucleotides designed by ArrayOligoSelector

manufacture_protocol: As described at http://derisilab.ucsf.edu


title: Spalax_Mouse_15K_UofIL

status: Public on Jul 14 2006

city: Urbana

first: Mark

middle: Robert

last: Band

address: 1201 W. Gregory Dr

department: Biotechnology

institute: University of Illinois

organism:
Mus musculus
Nannospalax ehrenbergi

first: Aaron

last: Avivi

first: Leonid

last: Brodsky

first: Eviatar

last: Nevo

manufacture_protocol: cDNA array created by amplification of the National Institute of Aging 15K clone set. All clones were PCR amplified using M13 forward and reverse primers, cleaned with millipore filter plates and printed in 3xSSC and 1.5M betaine with a Genomic Solutions OmniGrid 100 robot. Arrays were printed on Corning GAPSII amino coated slides. 32 Spalax sequences were added to the array.


title: CSIRO Wheat Barley 5K endosperm (wheatarrayII)

first: Andrew

last: Spriggs

description: Endosperm

first: Bryan

last: Clarke

first: Sadequr

last: Rahman


title: Drosophila sperm chip v1.0

city: Durham

first: Amanda

last: Moehring

department: DCMB/Biology

institute: Duke University

organism:
Drosophila mauritiana
Drosophila sechellia
Drosophila simulans

description: This set includes 52 oligonucleotides (3 alleles for each - D. simulans, D. mauritiana and D. sechellia) of 48 genes known or suspected to be involved in spermatogenesis, 2 housekeeping genes (Actin 5C and 18SrRNA) and 2 genes relevant to another study (CG9775 and 5-HT2); 111-458-mer cDNA; all 3 alleles of all 50 genes are spotted 4 times on the array (600 spots/array).

first: Mohamed

last: Noor

manufacture_protocol: As described by Duke Microarray Core Facility


title: Escherichia Coli Lambda Lysogen

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

organism: Escherichia coli

manufacturer: Arkin Lab, University of California at Berkeley

manufacture_protocol: cDNA probes were spotted onto SuperAmine glass slides using a Genomic Solutions OmniGrid robotic printer.  After printing, the cDNA probes were fixed onto the slides by UV cross-linking.


title: Arabidopsis Whole Genome Tiling Array 17-rc-3

status: Public on Jul 06 2006

city: La Jolla

middle: R.

last: Ecker

address: 10010 N. Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

organism: Arabidopsis thaliana

description: This Affymetrix array tiles the Arabidopsis genome end to end using in situ synthesized 25 bp oligonucleotides. The January 2002 version of the Arabidopsis genome sequence was originally used to make these chips, however, the position coordinates in the table are remapped on and refer to the Arabidopsis genome version 6 sequence.

first: Chris

last: Palm

first: A

last: Theologis

first: Ronald

last: Davis

first: Huaming

last: Chen

manufacture_protocol: See manufacturer's web site


title: Arabidopsis Whole Genome Tiling Array 17-rc-2


title: Functional ID v2.0 Array 1

city: Boston

first: Julja

last: Burchard

state: MA

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

organism: Homo sapiens

first: Amit

middle: V

last: Kulkarni

first: John

last: Castle


title: Arabidopsis Whole Genome Tiling Array 17-rc-6

first: Joseph


title: Arabidopsis Whole Genome Tiling Array 17-rc-4


title: UHN Microarray Center Homo sapiens 1.6K

city: Montreal

first: Eduardo

last: Hernandez

state: Quebec

address: 3755 Cote-Sainte-Catherine Road

department: Molecular Oncology Group

institute: Lady Davis Institute for Medical Research (JGH)

manufacture_protocol: Manufacture protocol can be found at: www.microarray.ca


title: Arabidopsis Whole Genome Tiling Array 17-rc-5


title: Arabidopsis Whole Genome Tiling Array 17-6


title: Arabidopsis Whole Genome Tiling Array 17-4


title: CNIO Human Oncochip v2.0

status: Public on Jul 13 2006

city: Barcelona

first: Miriam

last: Molina-Arcas

address: Av. Diagonal, 645

department: Bioquimica i Biologia Molecular

country: Spain

institute: Universitat de Barcelona


title: UPENN_Canis familiaris_4.5K_v1.0

city: Philadelphia

first: Gerardo

middle: L.

last: Paez

state: PA

address: 3900 Delancey Street

department: Clinical Studies Philadelphia

institute: University of Pennsylvania

organism: Canis lupus familiaris

manufacturer: Microarray Core Facilty, School of Medicine, UPENN.

first: Barbara

last: Zangerl

first: Gustavo

middle: D

last: Aguirre

first: Mark

last: Band

manufacture_protocol: For microarray production, 3,931


title: Eurogentec L090D Yeast ORFs

city: Brussels

first: Bart

last: Scherens

address: Av. E. Gryson, 1

institute: IRMW-ULB

description: The yeast 5803 ORFs MicroArray is composed of 32 subgrids, which follow a pattern of 8 metarows and 4 metacolumns. Each subgrid contains 20 columns and 20 rows with a dot spacing of 200 µm. Probes are spotted as closed duplicates. In order to provide a friendly environment, the first subgrid row on each array metarow contains all the normalization controls, which include the controls with serial dilution of the Renilla LuxA cDNA PCR product. In addition to this control, four serial dilutions of the sonicated yeast S288c genomic DNA are also located in the corner subgrids of the MicroArray.

manufacture_protocol:
Comparative genome analysis of 6213 predicted Saccharomyces cerevisiae open reading frame (ORF) products with 13 yeast genome sequence related species proposed the elimination of 612 predicted ORFs that are not real genes (A. Malpertuy et al, FEBS Letters, Volume 487, 22 December 2000). The study identified the presence of 50 new genes.
Specific pair of primers was designed by Pasteur Institute, Paris to amplify all 5803 ORFs non-spurious coding sequences. The primers were selected carefully to amplify only a specific region of each ORF.
Universal sequences of 15 bases were incorporated on the 5' of each specific forward and reverse primer.
The two-step PCR method has been employed to generate 5' amino-modified PCR for covalent attachment to the aldehyde-coated support.
All the amplicons have an average length of 300 bp and they were controlled systematically by electrophoresis on agarose gels.


title: SAGE:16:NlaIII:Bombyx mori

status: Public on Jul 10 2006

last: GEO

organism: Bombyx mori

technology: SAGE NlaIII

description: This is a virtual platform for SAGE libraries generated for Bombyx mori using NlaIII as an anchor enzyme.

distribution: virtual


title: INSERM Rat Operon Pronto plus Systems 6 Oligoarray

city: Toulouse

first: Philippe

last: Rouet

address: 1 Ave Jean Poulhes

department: Cardiology

institute: INSERM U1048

organism: Rattus norvegicus

description: Deposition on each glass slide of the cDNA from one lean with one obese SHHF rats

manufacture_protocol:
Rat oligos (set V3 from OPERON, 73 plates/96 wells) were loaded at 300 pmol/wells. Oligos were resuspended in 20µl 3X SSC buffer (concentration finale 20µM), plates were shaken  and frozen before spotting. Pirot to spotting, plates are defrozen one hour at room temperature and centrifuged. Spotting was performed as single spot on Ultragaps glass slides (CORNING) using Qarray mini robot (GENETIX). Atmosphere moisture was set at 50% and plates were cooled to 15°C to prevent drying. Spotting design was as follow:
48 pins therefore 48 grids
each grid contains 24x25 spots


title: UPENN_Canis familiaris_4.5k_v2

first: Sarah

last: Lindauer


title: Eurogentec C060C Yeast ORFs


title: scag_scai Sus scrofa 1.2K mono array

city: Castanet-Tolosan Cedex

first: Gwenola

last: Tosser-Klopp

address: Chemin de Borde-Rouge  BP 52627

institute: INRA

organism: Sus scrofa

manufacture_protocol: as described in Institute Labs manual


title: scag_scai Sus scrofa 4.6K triplicate array


title: Arabidopsis Whole Genome Tiling Array 17-rc-1

last: Ecker

first: Chris

last: Palm

first: A

last: Theologis


title: roo tiling and microRNA array (#2)

status: Public on Jul 03 2006

city: Worcester

first: Hervé

last: Seitz

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

organism: Drosophila melanogaster

first: Vasily

last: Vagin

first: Alla

last: Sigova

first: Chengjian

last: Li

first: Vladimir

last: Gvozdev

first: Phillip

last: Zamore

manufacture_protocol:
MicroRNA probes were designed by LC Sciences (based on Sanger Institute miRBase repository sequences on April 27, 2006). LNA-modified RNA probes were synthesized in situ using photogenerated acid coupled with conventional DMT chemistry (LNA-modification ensures Tm-normalization). Synthesis was performed on a µParaflo microfluidic chip.
See http://www.lcsciences.com for additionnal details.


title: Arabidopsis Whole Genome Tiling Array 17-3

first: Joseph

first: Ronald

last: Davis

first: Huaming

last: Chen


title: Arabidopsis Whole Genome Tiling Array 17-5


title: Su(Ste) tiling and microRNA array (#6)

manufacture_protocol:
MicroRNA probes were designed by LC Sciences (based on Sanger Institute miRBase repository sequences on January 12, 2006). LNA-modified RNA probes were synthesized in situ using photogenerated acid coupled with conventional DMT chemistry (LNA-modification ensures Tm-normalization). Synthesis was performed on a µParaflo microfluidic chip.
See http://www.lcsciences.com for additionnal details.


title: Arabidopsis Whole Genome Tiling Array 17-2


title: Arabidopsis Whole Genome Tiling Array 17-1


title: Su(Ste) tiling and microRNA array (#7)

manufacture_protocol:
MicroRNA probes were designed by LC Sciences (based on Sanger Institute miRBase repository sequences on August 2, 2005). LNA-modified RNA probes were synthesized in situ using photogenerated acid coupled with conventional DMT chemistry (LNA-modification ensures Tm-normalization). Synthesis was performed on a µParaflo microfluidic chip.
See http://www.lcsciences.com for additionnal details.


title: White tiling and microRNA array

manufacture_protocol:
MicroRNA probes were designed by LC Sciences (based on Sanger Institute miRBase repository sequences on November 17, 2005). LNA-modified RNA probes were synthesized in situ using photogenerated acid coupled with conventional DMT chemistry (LNA-modification ensures Tm-normalization). Synthesis was performed on a µParaflo microfluidic chip.
See http://www.lcsciences.com for additionnal details.


title: roo tiling and microRNA array

manufacture_protocol:
MicroRNA probes were designed by LC Sciences (based on Sanger Institute miRBase repository sequences on December 7, 2005). LNA-modified RNA probes were synthesized in situ using photogenerated acid coupled with conventional DMT chemistry (LNA-modification ensures Tm-normalization). Synthesis was performed on a µParaflo microfluidic chip.
See http://www.lcsciences.com for additionnal details.


title: piRNA sequences in rat

city: Waltham

first: Nelson

last: Lau

address: 415 South St MS029

institute: Brandeis University

technology: other

description: Sequences were analyzed and annotated for matches to the rat genome. See Supplemental Online Materials from Lau et al. Science. 2006 Jun 15; [Epub ahead of print] PMID: 16778019 for detailed protocol on data processing.

first: Anita

middle: G

last: Seto

first: Jinkuk

last: Kim

first: Satomi

last: Kuramochi-Miyagawa

first: Toru

last: Nakano

first: David

middle: P

last: Bartel

first: Robert

last: Kingston

manufacture_protocol: We constructed a cDNA library from small RNAs purified from Q column fractions of testes extracts. Briefly, gel-purified small RNAs from the column fractions were ligated with adaptor oligos on both 3' and 5' ends of the small RNAs. Reverse-transcription and PCR amplification was then performed on the ligated small RNAs to yield a cDNA library. This cDNA library was finally converted by PCR into a single-stranded DNA library compatible for coupling to beads on the 454 Life Sciences Genome Sequencer 20 System. Reads and sequences of the small RNAs were processed from linker sequences, examined for matches to the rat genome, and tallied.


title: Su(Ste) tiling and microRNA array (#4)

manufacture_protocol:
MicroRNA probes were designed by LC Sciences (based on Sanger Institute miRBase repository sequences on November 3, 2005). LNA-modified RNA probes were synthesized in situ using photogenerated acid coupled with conventional DMT chemistry (LNA-modification ensures Tm-normalization). Synthesis was performed on a µParaflo microfluidic chip.
See http://www.lcsciences.com for additionnal details.


title: BMFZ Mouse heart microarray 2005

status: Public on Jul 01 2006

city: Duesseldorf

first: Birgit

last: Andree

address: Moorenstr. 5

institute: BMFZ

description: epoxy glass slides (Eppendorf)

first: Thor

last: Gehrmann

first: Karl

last: Koehrer

first: Juergen

last: Mehrens

manufacture_protocol:
Amino-modified 70 mer oligonucleotides were either ordered from Eurogentec or Operon.
The design of the oligonucleotides was performed by Operon or was done with OligoWiz 1.0.
Oligonucleotides were spotted at a concentration of 50 pmol/ml in Qunatifoil II spotting buffer onto epoxy glass slides (Eppendorf) with a GMS 417 pin-and-ring arrayer (Affymetrix). Blocking of reactive groups was done according to the suppliers protocoll.


title: MouseGEM203caf

city: Maastricht

first: Marten H.

last: Hofker

address: P.O. Box 616

department: Molecular Genetics

country: Netherlands

institute: University Maastricht

manufacture_protocol:
Mouse GEM 2.03 produced by Incyte Genomics, Palo Alto, CA, USA.
References: Yue, H. et al., Nucleic Acids Research 2001, Vol. 29, No.8 e41.
Johston, R. et al., Genome Biol. 2004, 5(3): R19


title: UC Davis Singer Myxococcus xanthus 9.5K cDNA array

status: Public on Sep 17 2005

city: Davis

first: Mitchell

last: Singer

address: 1 Shields Ave

institute: The University of California, Davis

organism: Myxococcus xanthus

manufacture_protocol: spotted cDNA array


title: Genomic Research Laboratory Rickettsia conorii 0.7 k

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

organism: Rickettsia conorii

manufacturer: Unité des Rickettsies, CNRS-UMR6020, IFR48, Faculté de Médecine, 27, Bd Jean Moulin, Marseille, France

first: My-Van

last: La

first: Patrice

last: Francois

first: Clarisse

last: Rovery

first: Sylvianne

last: Robineau

first: Pascal

last: Barbry

first: Jacques

last: Schrenzel

first: Didier

last: Raoult

first: Patricia

last: Renesto

manufacture_protocol: A microarray including 129 targets specific for R. conorii was constructed by PCR amplification. These targets include 82 ORFs representing about 6% of R. conorii genome, and 47 intergenic spacers. Briefly, a specific amplification of selected targets was carried out usi printed onto glass slides (Corning® Gaps II Coated slide) by using a SDng oligonucleotide primers containing an universal sequences at the 5’-end (5’-CGACGCCCGCTGATA-3’ for forward / 5’-GTCCGGGAGCCATG-3’ for reverse). Following purification (MultiScreen PCR96 Filter Plate, Millipore, Billerica, MA, USA), amplicons (QIAquick 96-well purification kit ; QIAGEN, Courtaboeuf, France) were sequenced (3100 Genetic Analyzer, Applied Biosystems, Courtaboeuf, France) to check for the identity of amplified samples and processed in a second PCR run by using universal primers. The amplified DNA fragments were thenDC-2 robot (Bio-Rad, Marnes-la-Coquette, France). The spotted slides were cross linked by using a UV Stratalinker (Stratagene, La Jolla, CA, USA) each at a total energy of 250 mJ and stored in a dry environment at room temperature for at least 12 hours. The quality of printing (spot morphology and intensity) was checked by Syto-9 staining (Molecular Probes, Eugene, OR).


title: Su(Ste) tiling and microRNA array (#5)

first: Hervé

last: Seitz

first: Vasily

last: Vagin

first: Alla

last: Sigova

first: Chengjian

last: Li

first: Vladimir

last: Gvozdev

first: Phillip

last: Zamore


title: Su(Ste) tiling and microRNA array (#3)


title: Su(Ste) tiling and microRNA array (#2)

manufacture_protocol:
MicroRNA probes were designed by LC Sciences (based on Sanger Institute miRBase repository sequences on September 7, 2005). LNA-modified RNA probes were synthesized in situ using photogenerated acid coupled with conventional DMT chemistry (LNA-modification ensures Tm-normalization). Synthesis was performed on a µParaflo microfluidic chip.
See http://www.lcsciences.com for additionnal details.


title: Toulouse Genopole Yeast ORFs

first: Bart

last: Scherens

organism: Saccharomyces cerevisiae

description: 32 subarrays (spots organised in 22 rows and 22 columns per subarray) distributed in 8 rows and 4 columns of subarrays.

manufacture_protocol:
see website "http://biopuce.insa-toulouse.fr/"
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title: SAGE:10:NlaIII:Lolium perenne

status: Public on Jul 02 2006

last: GEO

organism: Lolium perenne

description: This is a virtual platform for SAGE libraries generated for Lolium perenne using NlaIII as an anchor enzyme.


title: Su(Ste) tiling and microRNA array (#1)


title: VUMC MACF human 19K oligo v33

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
- oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions
- oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome
- all plates were printed twice (duplicate spots)

first: Paul

last: van den IJssel

first: Bauke

last: Ylstra

manufacture_protocol: The Human Release 1.0 oligonucleotide library, containing 18861 60-mer oligonucleotides representing 17260 unique genes as designed by Compugen (San Jose, CA, USA) was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 µM concentration in 150 mM sodium phosphate buffer pH 8.5. 384-well plates 1-39 containing 14485 unique oligonucleotides were spotted in duplo onto CodeLink™ slides (Amersham Biosciences) using an OmniGrid® 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: Nimblegen Human custom array

status: Public on Jul 04 2006

city: Hannover

first: Jürgen

last: Borlak

address: Nikolai-Fuchs-Strasse 1

institute: Fraunhofer Institut

manufacture_protocol:
The manufacturer protocol used for the Nimblegen human custom array was performed according to the experimental protocol described in: Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8.
Silanization of microscope slides.
Microscope slides were prepared according to the method of McGall and colleagues8. Briefly, soda lime glass microscope slides (Fisher Scientific Co., Itasca, IL) were soaked in a bath of Nanostrip (Cyantek, Fremont, CA) for 15 min, water, 1% (vol/vol) aqueous HCl for 1 min, 70°C 10% (wt/vol) aqueous NaOH for 3 min, water, 1% (vol/vol) solution of N-(3-(triethoxysilyl)-propyl)-4-hydroxybutyramide (Lancaster Synthesis, Windham, NH) for 15 min. The slides were then rinsed in 2-propanol for 5 min, water for 5 min, and then dried in a spin dryer for 5 min at 100°C under nitrogen. Slides were then stored desiccated at -20°C until use.
Synthesis of photolabile phosphoramidites.
The MeNPOC-HEG-cyanoethylphosphoramidite (CEP) and MeNPOC-base-CEPs were synthesized according to the protocol described by McGall and colleagues8. Briefly, 3,4-(methylenedioxy)acetophenone (Aldrich Chemical Co., Milwaukee, WI) was reacted with glacial acetic acid and 70% (vol/vol) HNO3 to produce methyl 3,4-(methylenedioxy)-6-nitrophenyl ketone. This molecule was reacted with sodium borohydride to produce (R,S)-1-(3,4-(methylenedioxy)-6-nitrophenyl)ethanol, which was then reacted with phosgene to produce (R,S)-1-(3,4-(methylenedioxy)-6-nitrophenyl)ethyl chloroformate (MeNPOC-Cl). This molecule was attached to hexaethylglycol and A(PAC), C(ibu), and G(ibu). These molecules were then converted to phosphoramidites by reacting with 2-cyanoethyl N,N,N',N'-tetraisopropylphosphorodiamidite and diisopropyl ammonium tetrazolide to produce the final products.
Coating of silanized microscope slides with MeNPOC-HEG.
Silanized microscope slides were attached to the reaction chamber and MeNPOC-HEG-CEP (50 mM) was delivered to the chamber via a standard DNA synthesizer (ABI 392), which was programmed to deliver reagents for DNA synthesis.
Patterned photodeprotection of MeNPOC.
The MAS was used to deliver the desired photon using control software (Modularis, Chicago, IL) that designates the desired exposure time and displays the appropriate virtual mask at the correct time and place. The intensities given above for various experiments were measured at the image plane for an all-white image using an International Light UV Dosimeter (Newburyport, MA) with a calibrated detector for 365 nm radiation. A typical intensity was 19.5 mW/cm2 for a lamp with 227 h of prior use. (Intensity increased to 28.5 mW/cm2 with a new Hg arc lamp).
Staining of deprotected hydroxyl groups with FluorePrime fluorescein amidite.
A mixture of FluorePrime (Amersham Pharmacia Biotech, Uppsala, Sweden) and DMT-Thymidine-CEP (Glen Research, Sterling, VA) 1:10 was diluted with anhydrous acetonitrile to a final concentration of 50 mM amidites. This mixture was delivered to the chamber via the DNA synthesizer during a cycle of standard phosphoramidite chemistry. After coupling of the Fluoreprime to the microscope slide, the slide was removed from the chamber. The slide was soaked for 15 min in a solution of ethylenediamine−EtOH (1:1) to remove protecting groups on the phosphate and fluorescein molecules and then rinsed for 5 min in water and spun dry.
Visualization of patterned fluorescein-labeled slides.
The slides were viewed with a Bio-Rad (Bio-Rad Laboratories, Hercules, CA) MRC-1024 laser scanning confocal microscope. The 488 nm line of an Ar/Kr laser was the excitation source, and a 530 nm bandpass filter was used in front of a photomultiplier tube to collect the emission from the fluorescein. Images were acquired using both direct-mode and time-domain Kalman filtering of five image frames.
Oligonucleotide array fabrication and hybridization.
The MAS was used to pattern MeNPOC-phosphoramidites in dioxane. The oligonucleotide 5'-AGGTCATTACAGCGAGAG-3' was selected from the Arabidopsis CPK6 gene using the Primer3 program10 developed at Massachusetts Institute of Technology, Cambridge, MA). Three additional 18-mers were created by changing one, two, or three bases of the original sequence. After synthesis of the oligonucleotide probes, the slide was soaked in a solution of ethylenediamine−ethanol (1:1) for 2 h to remove the protecting group and then washed with water. The slide was hybridized with 200 l of 100 nM synthetic biotin-labeled oligonucleotide target 5'-biotinCTCTCGCTGTAATGACCT-3' (Genosys Biotechnologies, The Woodlands, TX). The hybridization solution contained 100 mM (2-[N-Morpholino]ethanesulphonic acid (MES), 1 M NaCl, 20 mM EDTA, and 0.01% (vol/vol) Tween 20. The hybridization was carried out overnight at room temperature in a hybridization chamber consisting of the DNA chip slide, a Kalrez (DuPont Dow Elastomers, Newark, DE) gasket, and a glass coverslip. After hybridization was complete, the array wash washed with a nonstringent wash buffer (6 SSPE [0.9M NaCl, 60 mM HaH 2PO4, 6 mM EDTA (pH7.4)]) and 0.01% [vol/vol] Tween 20) and stained with streptavidin phycoerythrin (10 g/ml) in 100 mM MES, 1 M Na +, and 0.05% Tween 20 for 30 min. The array was then washed with the nonstringent buffer and imaged with a Bio-Rad confocal microscope.


title: DKFZ Homo sapiens 6k-array, version 3/4, upgrade

status: Public on Dec 31 2005

city: Heidelberg

first: Frank

last: Mendrzyk

institute: German Cancer Research Center (DKFZ)

first: Bernhard

last: Radlwimmer

first: Peter

last: Lichter

manufacture_protocol: Whole-genome BAC-array. Isolated BAC-DNA was amplified by two-step DOP-PCR. PCR products were dissolved in 3xSSC, 1.5M betaine and spotted as triplicates on epoxysilane-coated slides.


title: Small RNA identification in Arabidopsis thaliana using modified MPSS

status: Public on Sep 02 2005

first: Blake

middle: C.

last: Meyers

address: 451 Health Sciences Dr.

department: UC Davis Genome Center

institute: University of California - Davis

technology: MPSS

description:
All MPSS was performed essentially as described by Brenner et al. (Nat Biotechnol. 2000 18:630).
The specific modifications to the method for the MPSS sequencing of small RNAs are described in the paper associated with this dataset  (Lu et al., 2005).
The signatures with "flag = 1" match to tRNAs, rRNAs, snoRNAs and snRNAs.


title: Center for Functional Analysis of Human Genome Human Incyte 10K

status: Public on Oct 07 2005

city: Daejeon

first: Heun-Sik

last: Lee

address: 52 Eoeun-dong, Yuseong-gu

country: South Korea

institute: Korea Reaearch Institute of Bioscience and Biotechnology

manufacturer: The Center for Functional Analysis of Human Genome

manufacture_protocol: cDNA microarrays were fabricated in our core facility using a robotic arrayer (PixSYS 5500, Cartesian; Ann Arbor, MI). The 10K microarray contains 10,336 genes (10K) from Incyte Unigene (Incyte,Wilmington,DE) (http://21cgenome.kribb.re.kr/html/2004_new/genome_php/cdna/cdna_list.htm). All the clones were verified by sequencing in our facility. The cDNA inserts were amplified by PCR, and after purification, spotted onto silylated glass slides (CSS-100; Telechem, Sunnyvale, CA). Each microarray slide contained control genes to normalize the effect of different fluorescent dyes.


title: Rat liver oligo array

status: Public on Jan 28 2005

city: Columbia

first: Sachin

middle: S

last: Bhusari

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: Univ of Missouri

description:
The oligos were obtained commercially from MWG Biotech's Rat liver oligo set. Microarrays were prepared by printing 1,353 oligos, 50 mers in length, representing rat genes expressed in liver on Pan epoxy glass slides (MWG Biotech AG, Ebersberg, Germany). The arrays also contained 10 arabidopsis genes, each of them printed 10 times across the array as external controls (Spot report oligoTM, Stratagene, Cedar Creek, Texas). Blank spots and 3X SSC were used as negative controls. A robotic microarray printer with 16 printing tips was used to spot the oligos. The rat liver oligo arrays have a total of 1,920 spots and are organized in 16 blocks arrayed in four rows and four columns. Each block has 120 spots arranged in 10 rows and 12 columns.
Keywords = Oligos
Keywords = Microarray

first: Eric

last: Antoniou